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- PDB-11aa: Yeast co-transcriptional pre-60S assembly intermediate Nop12 RNP -

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Basic information

Entry
Database: PDB / ID: 11aa
TitleYeast co-transcriptional pre-60S assembly intermediate Nop12 RNP
Components
  • (60S ribosomal protein ...) x 4
  • (Nucleolar protein ...) x 2
  • (Ribosome biogenesis protein ...) x 4
  • 25S ribosomal RNA
  • 5.8S ribosomal RNA
  • ATP-dependent RNA helicase HAS1
  • Internal transcribed spacer 2 ITS2
  • Pescadillo homolog
  • Proteasome-interacting protein CIC1
  • rRNA-processing protein EBP2
KeywordsRIBOSOME / ribosome biogenesis / co-transcriptional assembly / RNA-binding protein / nucleolar RNP
Function / homology
Function and homology information


snoRNA release from pre-rRNA / nuclear division / exonucleolytic trimming to generate mature 5'-end of 5.8S rRNA from tricistronic rRNA transcript (SSU-rRNA, 5.8S rRNA, LSU-rRNA) / endonucleolytic cleavage in ITS1 upstream of 5.8S rRNA from tricistronic rRNA transcript (SSU-rRNA, 5.8S rRNA, LSU-rRNA) / preribosome / PeBoW complex / ATP-dependent activity, acting on RNA / rRNA primary transcript binding / maturation of 5.8S rRNA from tricistronic rRNA transcript (SSU-rRNA, 5.8S rRNA, LSU-rRNA) / cytosolic large ribosomal subunit assembly ...snoRNA release from pre-rRNA / nuclear division / exonucleolytic trimming to generate mature 5'-end of 5.8S rRNA from tricistronic rRNA transcript (SSU-rRNA, 5.8S rRNA, LSU-rRNA) / endonucleolytic cleavage in ITS1 upstream of 5.8S rRNA from tricistronic rRNA transcript (SSU-rRNA, 5.8S rRNA, LSU-rRNA) / preribosome / PeBoW complex / ATP-dependent activity, acting on RNA / rRNA primary transcript binding / maturation of 5.8S rRNA from tricistronic rRNA transcript (SSU-rRNA, 5.8S rRNA, LSU-rRNA) / cytosolic large ribosomal subunit assembly / Ribosome Quality Control (RQC) complex extracts and degrades nascent peptide / Major pathway of rRNA processing in the nucleolus and cytosol / PELO:HBS1L and ABCE1 dissociate a ribosome on a non-stop mRNA / SRP-dependent cotranslational protein targeting to membrane / GTP hydrolysis and joining of the 60S ribosomal subunit / ribosomal large subunit binding / Formation of a pool of free 40S subunits / Nonsense Mediated Decay (NMD) independent of the Exon Junction Complex (EJC) / preribosome, large subunit precursor / proteasome binding / Nonsense Mediated Decay (NMD) enhanced by the Exon Junction Complex (EJC) / L13a-mediated translational silencing of Ceruloplasmin expression / ribonucleoprotein complex binding / 90S preribosome / maturation of LSU-rRNA / proteasome complex / protein catabolic process / nuclear periphery / ribosomal large subunit biogenesis / maturation of SSU-rRNA from tricistronic rRNA transcript (SSU-rRNA, 5.8S rRNA, LSU-rRNA) / maturation of LSU-rRNA from tricistronic rRNA transcript (SSU-rRNA, 5.8S rRNA, LSU-rRNA) / rRNA processing / nuclear envelope / ribosomal small subunit biogenesis / 5S rRNA binding / ribosomal large subunit assembly / large ribosomal subunit rRNA binding / cytosolic large ribosomal subunit / cytoplasmic translation / protein-macromolecule adaptor activity / RNA helicase activity / rRNA binding / RNA helicase / structural constituent of ribosome / mRNA binding / nucleolus / ATP hydrolysis activity / DNA binding / RNA binding / nucleoplasm / ATP binding / identical protein binding / nucleus / cytosol / cytoplasm
Similarity search - Function
Nop12, RNA recognition motif 1 / : / Ribosome biogenesis protein 15, RNA recognition motif / Eukaryotic rRNA processing / Eukaryotic rRNA processing protein EBP2 / Ribosome biogenesis protein Nop16 / Ribosome biogenesis protein Nop16 / Ribosome biogenesis protein BRX1 / DDX18/Has1, DEAD-box helicase domain / Domain of unknown function DUF4217 ...Nop12, RNA recognition motif 1 / : / Ribosome biogenesis protein 15, RNA recognition motif / Eukaryotic rRNA processing / Eukaryotic rRNA processing protein EBP2 / Ribosome biogenesis protein Nop16 / Ribosome biogenesis protein Nop16 / Ribosome biogenesis protein BRX1 / DDX18/Has1, DEAD-box helicase domain / Domain of unknown function DUF4217 / ATP-dependent rRNA helicase SPB4-like, C-terminal extension / DUF4217 / BOP1, N-terminal domain / WD repeat BOP1/Erb1 / BOP1NT (NUC169) domain / BOP1NT (NUC169) domain / Pescadillo / Pescadillo N-terminus / BRCT domain / Brix domain / Brix domain / Brix domain profile. / Brix / DEAD-box subfamily ATP-dependent helicases signature. / ATP-dependent RNA helicase DEAD-box, conserved site / RNA helicase, DEAD-box type, Q motif / DEAD-box RNA helicase Q motif profile. / breast cancer carboxy-terminal domain / BRCT domain profile. / BRCT domain / Ribosomal protein L13e, conserved site / Ribosomal protein L13e signature. / BRCT domain superfamily / Ribosomal protein L1-like / Ribosomal protein L1/ribosomal biogenesis protein / Ribosomal protein L1p/L10e family / Ribosomal protein L13e / Ribosomal protein L13e / Ribosomal protein L36e signature. / Ribosomal protein L7A/L8 / Ribosomal protein L36e / Ribosomal protein L36e domain superfamily / Ribosomal protein L36e / Ribosomal protein L15e, conserved site / Ribosomal protein L15e signature. / DEAD/DEAH box helicase domain / DEAD/DEAH box helicase / Ribosomal protein L7Ae conserved site / Ribosomal protein L7Ae signature. / Ribosomal_L15e / Ribosomal protein L15e / Ribosomal protein L15e core domain superfamily / Ribosomal L15 / Ribosomal protein L7, eukaryotic/archaeal / Ribosomal protein L7/L30 / RNA recognition motif / Ribosomal protein L7Ae/L8/Nhp2 family / RNA recognition motif / : / Eukaryotic RNA Recognition Motif (RRM) profile. / RNA recognition motif domain / RNA-binding domain superfamily / Ribosomal protein L7Ae/L30e/S12e/Gadd45 / Ribosomal protein L7Ae/L30e/S12e/Gadd45 family / Helicase conserved C-terminal domain / 50S ribosomal protein L30e-like / Ribosomal protein L30, conserved site / Ribosomal protein L30 signature. / helicase superfamily c-terminal domain / Ribosomal protein L30, ferredoxin-like fold domain / Ribosomal protein L30p/L7e / Ribosomal protein L30, ferredoxin-like fold domain superfamily / WD domain, G-beta repeat / Superfamilies 1 and 2 helicase C-terminal domain profile. / Superfamilies 1 and 2 helicase ATP-binding type-1 domain profile. / DEAD-like helicases superfamily / Helicase, C-terminal / Helicase superfamily 1/2, ATP-binding domain / Ribosomal protein L23/L15e core domain superfamily / Nucleotide-binding alpha-beta plait domain superfamily / WD40 repeat, conserved site / Trp-Asp (WD) repeats signature. / Trp-Asp (WD) repeats profile. / Trp-Asp (WD) repeats circular profile. / WD40 repeats / WD40 repeat / WD40-repeat-containing domain superfamily / WD40/YVTN repeat-like-containing domain superfamily / P-loop containing nucleoside triphosphate hydrolase
Similarity search - Domain/homology
: / : / : / RNA / RNA (> 10) / RNA (> 100) / RNA (> 1000) / Large ribosomal subunit protein eL36A / Large ribosomal subunit protein eL15A / Large ribosomal subunit protein eL8A ...: / : / : / RNA / RNA (> 10) / RNA (> 100) / RNA (> 1000) / Large ribosomal subunit protein eL36A / Large ribosomal subunit protein eL15A / Large ribosomal subunit protein eL8A / rRNA-processing protein EBP2 / Proteasome-interacting protein CIC1 / Nucleolar protein 16 / Ribosome biogenesis protein RLP7 / Pescadillo homolog / Ribosome biogenesis protein 15 / ATP-dependent RNA helicase HAS1 / Ribosome biogenesis protein ERB1 / Nucleolar protein 12 / Ribosome biogenesis protein BRX1 / Large ribosomal subunit protein eL13A
Similarity search - Component
Biological speciesSaccharomyces cerevisiae S288C (yeast)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 2.78 Å
AuthorsPiwowarczyk, R. / Klinge, S.
Funding support United States, 2items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)5R01GM145950-03 United States
Chan Zuckerberg Initiative2023-332391 United States
CitationJournal: bioRxiv / Year: 2026
Title: Mechanism for the initiation of co-transcriptional pre-60 assembly.
Authors: Rafal Piwowarczyk / Sebastian Klinge
Abstract: Eukaryotic ribosomal large subunit (60 ) assembly requires an internal transcribed spacer 2 (ITS2) to license both nucleolar and nuclear pre-60 assembly intermediates. The underlying molecular ...Eukaryotic ribosomal large subunit (60 ) assembly requires an internal transcribed spacer 2 (ITS2) to license both nucleolar and nuclear pre-60 assembly intermediates. The underlying molecular mechanisms responsible for nucleation of pre-60 assembly, quality control, and installation of ITS2 during co-transcriptional stages remain unknown. Here we report the earliest co-transcriptional assembly intermediates of the eukaryotic 60 subunits. Together with biochemical assays, our data reveal the architecture of co-transcriptional pre-60 assembly initiation and progression, as well as the molecular logic of an assembly checkpoint. This study highlights an evolutionary solution by which complex RNA folding processes can be parallelized and integrated via biological AND-gating.
History
DepositionFeb 13, 2026Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jul 1, 2026Provider: repository / Type: Initial release
Revision 1.0Jul 1, 2026Data content type: EM metadata / Data content type: EM metadata / Provider: repository / Type: Initial release
Revision 1.0Jul 1, 2026Data content type: Image / Data content type: Image / Provider: repository / Type: Initial release
Revision 1.0Jul 1, 2026Data content type: Primary map / Data content type: Primary map / Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
1: 25S ribosomal RNA
2: 5.8S ribosomal RNA
3: Internal transcribed spacer 2 ITS2
7: Nucleolar protein 16
G: 60S ribosomal protein L8-A
H: Nucleolar protein 12
K: Proteasome-interacting protein CIC1
L: 60S ribosomal protein L13-A
N: 60S ribosomal protein L15-A
b: Ribosome biogenesis protein BRX1
i: 60S ribosomal protein L36-A
m: rRNA-processing protein EBP2
n: Pescadillo homolog
o: Ribosome biogenesis protein 15
p: ATP-dependent RNA helicase HAS1
s: Ribosome biogenesis protein ERB1
t: Ribosome biogenesis protein RLP7
hetero molecules


Theoretical massNumber of molelcules
Total (without water)1,795,10822
Polymers1,794,98717
Non-polymers1225
Water00
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: electron microscopy, not applicable
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1

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Components

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RNA chain , 3 types, 3 molecules 123

#1: RNA chain 25S ribosomal RNA


Mass: 1097493.875 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Saccharomyces cerevisiae S288C (yeast) / References: GenBank: 831416132
#2: RNA chain 5.8S ribosomal RNA


Mass: 51012.129 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Saccharomyces cerevisiae S288C (yeast) / References: GenBank: 1669301379
#3: RNA chain Internal transcribed spacer 2 ITS2


Mass: 74308.391 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Saccharomyces cerevisiae S288C (yeast) / References: GenBank: 2771401504

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Nucleolar protein ... , 2 types, 2 molecules 7H

#4: Protein Nucleolar protein 16


Mass: 26954.447 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Saccharomyces cerevisiae S288C (yeast) / References: UniProt: P40007
#6: Protein Nucleolar protein 12


Mass: 52046.086 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Saccharomyces cerevisiae S288C (yeast) / References: UniProt: Q08208

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60S ribosomal protein ... , 4 types, 4 molecules GLNi

#5: Protein 60S ribosomal protein L8-A / L4 / L4-2 / L7a-1 / Large ribosomal subunit protein eL8-A / Maintenance of killer protein 7 / RP6 / YL5


Mass: 28175.820 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Saccharomyces cerevisiae S288C (yeast) / References: UniProt: P17076
#8: Protein 60S ribosomal protein L13-A / Large ribosomal subunit protein eL13-A


Mass: 22604.164 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Saccharomyces cerevisiae S288C (yeast) / References: UniProt: Q12690
#9: Protein 60S ribosomal protein L15-A / L13 / Large ribosomal subunit protein eL15-A / RP15R / YL10 / YP18


Mass: 24482.357 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Saccharomyces cerevisiae S288C (yeast) / References: UniProt: P05748
#11: Protein 60S ribosomal protein L36-A / L39 / Large ribosomal subunit protein eL36-A / YL39


Mass: 11151.259 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Saccharomyces cerevisiae S288C (yeast) / References: UniProt: P05745

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Protein , 4 types, 4 molecules Kmnp

#7: Protein Proteasome-interacting protein CIC1 / Core interacting component 1


Mass: 42596.691 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Saccharomyces cerevisiae S288C (yeast) / References: UniProt: P38779
#12: Protein rRNA-processing protein EBP2 / EBNA1-binding protein homolog


Mass: 49842.613 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Saccharomyces cerevisiae S288C (yeast) / References: UniProt: P36049
#13: Protein Pescadillo homolog / Nucleolar protein 7 / Ribosomal RNA-processing protein 13


Mass: 69984.148 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Saccharomyces cerevisiae S288C (yeast) / References: UniProt: P53261
#15: Protein ATP-dependent RNA helicase HAS1 / Helicase associated with SET1 protein 1


Mass: 56798.348 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Saccharomyces cerevisiae S288C (yeast) / References: UniProt: Q03532, RNA helicase

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Ribosome biogenesis protein ... , 4 types, 4 molecules bost

#10: Protein Ribosome biogenesis protein BRX1


Mass: 33585.414 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Saccharomyces cerevisiae S288C (yeast) / References: UniProt: Q08235
#14: Protein Ribosome biogenesis protein 15 / Nucleolar protein 15


Mass: 25499.186 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Saccharomyces cerevisiae S288C (yeast) / References: UniProt: P53927
#16: Protein Ribosome biogenesis protein ERB1 / Eukaryotic ribosome biogenesis protein 1


Mass: 91830.609 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Saccharomyces cerevisiae S288C (yeast) / References: UniProt: Q04660
#17: Protein Ribosome biogenesis protein RLP7 / Ribosomal protein L7-like


Mass: 36621.074 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Saccharomyces cerevisiae S288C (yeast) / References: UniProt: P40693

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Non-polymers , 1 types, 5 molecules

#18: Chemical
ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: Mg

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Details

Has ligand of interestN
Has protein modificationN

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Experimental details

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Experiment

ExperimentMethod: ELECTRON MICROSCOPY
EM experimentAggregation state: PARTICLE / 3D reconstruction method: single particle reconstruction

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Sample preparation

ComponentName: Yeast co-transcriptional pre-60S assembly intermediate Nop12 RNP
Type: RIBOSOME / Entity ID: #1-#17 / Source: NATURAL
Molecular weightExperimental value: NO
Source (natural)Organism: Saccharomyces cerevisiae S288C (yeast)
Buffer solutionpH: 7.5
SpecimenEmbedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
Specimen supportGrid material: GOLD / Grid mesh size: 400 divisions/in. / Grid type: Quantifoil R3.5/1
VitrificationInstrument: FEI VITROBOT MARK IV / Cryogen name: ETHANE

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Electron microscopy imaging

Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company
MicroscopyModel: TFS KRIOS
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: FLOOD BEAM
Electron lensMode: BRIGHT FIELD / Nominal defocus max: 1700 nm / Nominal defocus min: 700 nm
Image recordingElectron dose: 51 e/Å2 / Film or detector model: GATAN K3 (6k x 4k)

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Processing

EM software
IDNameVersionCategory
1cryoSPARCparticle selection
2crYOLOparticle selection
3SerialEMimage acquisition
5cryoSPARCCTF correction
10cryoSPARCinitial Euler assignment
11cryoSPARCfinal Euler assignment
12cryoSPARCclassification
13cryoSPARC3D reconstruction
14ISOLDEmodel refinement
15PHENIX1.19.1_4122model refinement
CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
3D reconstructionResolution: 2.78 Å / Resolution method: OTHER / Num. of particles: 443499 / Symmetry type: POINT
Atomic model buildingProtocol: RIGID BODY FIT / Space: REAL
Atomic model buildingPDB-ID: 8E5T

8e5t


Accession code: 8E5T / Source name: PDB / Type: experimental model
RefinementHighest resolution: 2.78 Å
Stereochemistry target values: REAL-SPACE (WEIGHTED MAP SUM AT ATOM CENTERS)
Refine LS restraints
Refine-IDTypeDev idealNumber
ELECTRON MICROSCOPYf_bond_d0.00230836
ELECTRON MICROSCOPYf_angle_d0.50343262
ELECTRON MICROSCOPYf_dihedral_angle_d9.8347181
ELECTRON MICROSCOPYf_chiral_restr0.0375098
ELECTRON MICROSCOPYf_plane_restr0.0044182

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